Abstract Objective To investigate if an association exists between motion artefacts on brain MRI and comprehension, co-ordination, or hyperactivity scores in children aged 6–8 years, cooled for neonatal encephalopathy (cases) and controls. Methods Case children (n = 50) without cerebral palsy were matched with 43 controls for age, sex, and socioeconomic status. Children underwent T1-weighted (T1w), diffusion-weighted image (DWI) brain MRI and cognitive, behavioural, and motor skills assessment. Stepwise multivariable logistic regression assessed associations between unsuccessful MRI and comprehension (including Weschler Intelligence Scale for Children (WISC-IV) verbal comprehension, working memory, processing speed and full-scale IQ), co-ordination (including Movement Assessment Battery for Children (MABC-2) balance, manual dexterity, aiming and catching, and total scores) and hyperactivity (including Strengths and Difficulties Questionnaire (SDQ) hyperactivity and total difficulties scores). Results Cases had lower odds of completing both T1w and DWIs (OR: 0.31, 95% CI 0.11–0.89). After adjusting for case-status and sex, lower MABC-2 balance score predicted unsuccessful T1w MRI (OR: 0.81, 95% CI 0.67–0.97, p = 0.022). Processing speed was negatively correlated with relative motion on DWI (r = −0.25, p = 0.026) and SDQ total difficulties score was lower for children with successful MRIs (p = 0.049). Conclusions Motion artefacts on brain MRI in early school-age children are related to the developmental profile. Impact Children who had moderate/severe neonatal encephalopathy are less likely to have successful MRI scans than matched controls. Motion artefact on MRI is associated with lower MABC-2 balance scores in both children who received therapeutic hypothermia for neonatal encephalopathy and matched controls, after controlling for case-status and sex. Exclusion of children with motion artefacts on brain MRI can introduce sampling bias, which impacts the utility of neuroimaging to understand the brain–behaviour relationship in children with functional impairments.